Topological method query
I am attempting to apply the topological method from calc_topological.py to my own dataset, and I had a couple of questions I hoped that you could help me with.
Firstly, I assume that -bppml_non_conv
and -bppml_conv
refer to the site likelihoods calculated by bppml on the topology in which the putative convergent lineages are monophyletic and the topology in which they are not, respectively. If so, is there a simple way to produce these topologies, either through the utils in this repository or elsewhere?
Secondly, does the method first optimise the branch lengths on each of these topologies and then calculate the site likelihoods, or are the branch lengths left as is in the tree supplied to bppml?
Thanks in advance for your help,
Nathanael